Hi Martijn,
From you story i find it very hard to follow what you are trying to do and what your expectations are.
In general: in my experience merging in Mendix works ok, but you need to keep it simple. Every branch creates overhead from branching and merging, with the possibility of merge conflicts.
With a small team of only two developers, wouldn't it be possible to work in one branch eg a sprint branch or even just working in the main line? It save merges, branches and worries.
Otherwise i would recommend this source: https://www.mendix.com/blog/advanced-branching-merging-strategies-part-1-2/